Gita Sahgal, the former head of Amnesty International's gender unit. Photograph: Richard Saker

It has been a strange, disorientating and upsetting few months for Gita Sahgal. The former head of Amnesty International's gender unit was suspended in February after a very public and acrimonious dispute with her bosses. Two weeks ago she left it altogether. Her departure was provoked, according to a statement by Amnesty, by "irreconcilable differences".

The row – over Amnesty's links with Islamist pressure groups – has led to a succession of negative headlines for a body unused to such bad publicity. According to Sahgal, the affair was symptomatic of an organisation that has lost its moral bearings and risks alienating whole swathes of liberal sympathisers.

In her first newspaper interview since leaving the charity altogether, Sahgal delivers a withering critique of her former employers, describing the modern Amnesty's leadership as suffering from "ideological bankruptcy" and"misogyny". Although Amnesty is still one of the best known advocates of women's rights in the world, Sahgal told the Observer that an "atmosphere of terror" prevailed inside the organisation in which debate is suppressed and staff are cowed into accepting the prevailing line.

"I think the leadership is ideologically bankrupt, as has been shown in the handling of this," said Sahgal. "There have been systemic failures even before I went public. Questions need to be asked of the political and senior leadership. There is a deep misogyny in the human rights movement and the kinds of issues that women have to face tend to bring that out."

Sahgal was born in Bombay and is the daughter of novelist Nayantara Sahgal and great-niece of former Indian prime minister Jawaharlal Nehru. She became part of a feminist network that fought against rape and dowry laws. She moved to London to study, becoming heavily involved in Southall Black Sisters, the London-based group that campaigns against domestic violence, sexism and racism.

She became head of Amnesty's gender unit in 2003. The explosive falling out in one of the world's leading human rights organisations took place after the publication of an e-mail Sahgal sent to the leadership, complaining that Amnesty had become too closely linked to a "pro-jihadi group". The email appeared in a national newspaper in February. Sahgal claimed the charity's links with Moazzam Begg, a former inmate at Guantánamo Bay, and his group Cageprisoners were undermining its campaign for women's rights.

Begg, she claimed in the leaked email, was "Britain's most famous supporter of the Taliban". She believed it was legitimate to give a platform to Begg's account of his experience of unlawful detention and torture, but his beliefs meant it was a "gross error" to associate Amnesty with his organisation.

"It's something that undermines every aspect of the work we have done on discrimination against minorities. I cannot underestimate the level of horror expressed throughout the global women's movement," she told the Observer.

The problem, for Sahgal, is Begg's championing the rights of "hate" preachers and alleged defence of the notoriously misogynistic Taliban, which has used its power to systematically suppress the rights of women.

After seven years in Amnesty championing women's rights, Sahgal felt deeply compromised by the platform afforded to Begg. She says many UN specialists, lawyers, philosophers and influential figures in the global women's rights movement have jumped to her defence since her suspension.

Some have threatened to cut their association with Amnesty, the world's oldest human rights group. Others are said to have withdrawn donations to the charity in support of Sahgal, who left the organisation two weeks ago.

Among the groups that have stepped forward to support her are the Human Rights Commission of Pakistan, Women Human Rights Defenders Coalition, Women Living Under Muslim Law and Inform, a Sri Lankan human rights organisation. Amnesty, which has 2.2 million members, has faced few stickier periods since it was was founded in London in 1961 to support prisoners of conscience.

"Women's groups are watching events with some anxiety," said Sahgal. "They are particularly appalled by what is happening and are very scared that the good relationships they have built up with people on women's rights issues with Amnesty all over the world are going to be under threat because of this".

She added: "People are very disturbed but also extremely worried about going up against Amnesty."

Sahgal first aired concerns over Amnesty's alliance with Cageprisoners in 2008. "I was completely ignored," she said. "There has never been a debate on this issue, even in the middle of this global crisis, inside Amnesty International. They, the leadership, were silencing and ignoring the issue."

Her confrontation with the Amnesty leadership, which she says exhibits "multiple systemic failures", has left her disillusioned and worried for its future, given a culture of quashing debate and a deliberate policy of "silence" towards contrary views. "There is a fault-line running through [Amnesty]," she says, "and this has been exposed on a range of issues wider than what Begg believes."

Amnesty disagrees. In a statement issued after Sahgal's comments were put to it, the organisation said: "Begg speaks powerfully from personal experience about the abuses there. He advocates effectively detainees' rights to due process, and does so within the same framework of universal human rights standards that we are promoting."

Amnesty does, though, concede that Begg holds other views, arguing that, for example, the jihadist ideology of the Taliban can be kept separate from defending human rights.

"On whether one should talk to the Taliban, or on the role of jihad in self-defence: are such views antithetical to human rights? Our answer is no, even if we may disagree with them."

It added that if any evidence emerged that Begg or Cageprisoners have promoted views antithetical to human rights it would disown its advocacy. Sahgal maintains that a number of experts recommend "caution" when dealing with Begg and that efforts should have been made to investigate him before working with him. Begg, for his part, has dismissed Sahgal's claims as "ludicrous" and says he champions women's rights.

Amnesty also refutes Sahgal's allegations that debate within the organisation is discouraged, stating: "We are an organisation of activists with strong and different views on how best to achieve our common goals; dissent is inevitable, indeed welcome. Decisions are reviewed."

But there can be little doubt that Sahgal's views have struck a chord with many who would normally consider themselves active backers of Amnesty.

Heavyweights supporters of her stance include author Salmon Rushdie and Yakin Erturk, a former United Nations expert on violence against women. Hina Jilani, a UN representative on human rights and Asma Jahangir, another key UN figure, are also believed to be deeply concerned. Nawal el-Saadawi, the Egyptian writer and activist, and the respected Bangladeshi barrister Sara Hossain have also backed her.

"Amnesty is trying to message this as my concern only," she says. "But a lot of people have been raising private questions, including those who have been involved with Amnesty for years. They are wondering what the hell is going on."